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Structural Bioinformatics of Proteins and Protein Complexes and Applications to Cancer Biology

Award Number: R35GM122517
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2017
PERIOD OF PERFORMANCE END DATE: 03/31/2028

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Structural Bioinformatics of Proteins and Protein Complexes and Applications to Cancer Biology - Project Summary/Abstract Structural biology has a fundamental role to play in the advancement of cancer biology and the development of cancer therapeutics. With the rapid developments in experimental structural determination (both crystallography and cryo-EM spectroscopy), structure prediction methods (primarily AlphaFold2 and RosettaFold), and molecular simulation methods, we are poised to bring new levels structural information to cancer research. In this project, we will analyze the structural variation and dynamics of protein families commonly associated with cancer development or targets of cancer therapeutics using existing clustering methods for protein loops and new unsupervised learning techniques from the field of deep learning. We will develop methods for using AlphaFold2 to predict the structures of active and inactive kinases using templates based on our classification of active and inactive states of kinases and multiple sequence alignments optimized for this task. In relevant cases, these structure predictions will include the N and C terminal tails and other domains which may interact with the kinase domains. We will integrate AlphaFold2 structure predictions of protein homo- and heterooligomeric complexes with our database of common interfaces and assemblies found across the structures of proteins in the PDB. Interactions observed in crystals that are replicated by AlphaFold2 present well-founded hypotheses for functional protein interactions. This will be applied specifically for all human kinases where homodimer interactions play an important role in activation and inhibition. We will continue our structural bioinformatics studies of antibodies and expand this work to T-cell receptors, and investigate the utility of deep learning methods for computational antibody and TCR design. Finally, we will bring new structure prediction technologies and our statistical analysis of protein structures to the ongoing research programs of laboratory and clinical colleagues at Fox Chase Cancer Center and Temple University School of Medicine.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $744,480 )
2025	2025	THE INSTITUTE FOR CANCER RESEARCH	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	001	8	4/4/2025	NON-COMPETING CONTINUATION	$744,480
2025	2024	THE INSTITUTE FOR CANCER RESEARCH	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	7	11/6/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $744,480

Issue Date FY: 2024 ( Subtotal = $744,480 )
2024	2024	THE INSTITUTE FOR CANCER RESEARCH	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	002	7	6/19/2024	NON-COMPETING CONTINUATION	$74,448
2024	2024	THE INSTITUTE FOR CANCER RESEARCH	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	001	7	3/12/2024	NON-COMPETING CONTINUATION	$670,032
2024	2021	THE INSTITUTE FOR CANCER RESEARCH	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	5	3/1/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $744,480

Issue Date FY: 2023 ( Subtotal = $744,480 )
2023	2023	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	6	5/24/2023	COMPETING CONTINUATION	$744,480
														Subtotal = $744,480

Issue Date FY: 2021 ( Subtotal = $692,227 )
2021	2021	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	5	3/15/2021	NON-COMPETING CONTINUATION	$692,227
														Subtotal = $692,227

Issue Date FY: 2020 ( Subtotal = $692,227 )
2020	2020	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	4	6/1/2020	NON-COMPETING CONTINUATION	$692,227
														Subtotal = $692,227

Issue Date FY: 2019 ( Subtotal = $677,420 )
2019	2019	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	3	3/26/2019	NON-COMPETING CONTINUATION	$677,420
														Subtotal = $677,420

Issue Date FY: 2018 ( Subtotal = $677,420 )
2018	2018	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	001	2	5/21/2018	NON-COMPETING CONTINUATION	$67,743
2018	2018	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	2	3/20/2018	NON-COMPETING CONTINUATION	$609,677
														Subtotal = $677,420

Issue Date FY: 2017 ( Subtotal = $556,946 )
2017	2017	INSTITUTE FOR CANCER RESEARCH, THE	333 COTTMAN AVE	PHILADELPHIA	PA	19111	PHILADELPHIA	USA	Biomedical Research and Research Training	000	1	3/30/2017	NEW	$556,946
														Subtotal = $556,946

Grand Total All Awards = $5,529,680

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Structural Bioinformatics of Proteins and Protein Complexes and Applications to Cancer Biology

Award Number: R35GM122517

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 04/01/2017

PERIOD OF PERFORMANCE END DATE: 03/31/2028

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